University of Southern California

Microscopy Core Facility

USC Stem Cell

Imaging Analysis and Visualization Software

Available on computer in TBD

Amira (Visualization Science Group)
Amira offers 3D image analysis and visualization for a wide variety of image data, including confocal light microscopy, CT and MicroCT, MRI, lightsheet, OPT, etc. It provides tools for image segmentation, 2D and 3D volumetric measurements, 3D reconstruction from 2D section data and neuron tracing.

Imaris (BitPlane)
Imaris enables 2D–4D image analysis and visualization. Analysis includes cell counting, cell tracking, neuron tracing image segmentation, co-localization and 4D movie generation.

VGStudio (VoluemGraphics)
VG Studio is sophisticated volume rendering software that enables fine control of visualizations through the manipulation of transfer functions, lights and shadows and a variety of rendering procedures.

MatLab (Mathworks)

Free downloads

ImageJ and FIJI
ImageJ and FIJI (FIJI Is Just ImageJ) are the “go to” imaging applications for general purpose image processing. ImageJ uses the BioFormats library and can open most vendor specific image file formats. Many image analysis tools and scripts have been written for ImageJ. Though the user interface is less refined than commercial software, ImageJ performs equally well in many cases.

ZEN Lite
Zen Lite facilitates the viewing of Zeiss native file formats, including .zvi, .czi and .lsm, and the conversion of images to standard formats from Zeiss formats.